CP-nets: From Theory to Practice

Conditional preference networks (CP-nets) exploit the power of ceteris paribus rules to represent preferences over combinatorial decision domains compactly. CP-nets have much appeal. However, their study has not yet advanced sufficiently for their widespread use in real-world applications. Known algorithms for deciding dominance---whether one outcome is better than another with respect to a CP-net---require exponential time. Data for CP-nets are difficult to obtain: human subjects data over combinatorial domains are not readily available, and earlier work on random generation is also problematic. Also, much of the research on CP-nets makes strong, often unrealistic assumptions, such as that decision variables must be binary or that only strict preferences are permitted. In this thesis, I address such limitations to make CP-nets more useful. I show how: to generate CP-nets uniformly randomly; to limit search depth in dominance testing given expectations about sets of CP-nets; and to use local search for learning restricted classes of CP-nets from choice data

Optical parametric oscillation with distributed feedback in cold atoms

There is currently a strong interest in mirrorless lasing systems, in which the electromagnetic feedback is provided either by disorder (multiple scattering in the gain medium) or by order (multiple Bragg reflection). These mechanisms correspond, respectively, to random lasers and photonic crystal lasers. The crossover regime between order and disorder, or correlated disorder, has also been investigated with some success. Here, we report one-dimensional photonic-crystal lasing (that is, distributed feedback lasing) with a cold atom cloud that simultaneously provides both gain and feedback. The atoms are trapped in a one-dimensional lattice, producing a density modulation that creates a strong Bragg reflection with a small angle of incidence. Pumping the atoms with auxiliary beams induces four-wave mixing, which provides parametric gain. The combination of both ingredients generates a mirrorless parametric oscillation with a conical output emission, the apex angle of which is tunable with the lattice periodicity

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Is vaccine the magic bullet for malaria elimination? A reality check

Malaria remains a major health burden especially for the developing countries. Despite concerted efforts at using the current control tools, such as bed nets, anti malarial drugs and vector control measures, the disease is accountable for close to a million deaths annually. Vaccines have been proposed as a necessary addition to the armamentarium that could work towards elimination and eventual eradication of malaria in view of their historical significance in combating infectious diseases. However, because malaria vaccines would work differently depending on the targeted parasite stage, this review addresses the potential impact various malaria vaccine types could have on transmission. Further, because of the wide variation in the epidemiology of malaria across the endemic regions, this paper proposes that the ideal approach to malaria control ought to be tailor-made depending on the specific context. Finally, it suggests that although it is highly desirable to anticipate and aim for malaria elimination and eventual eradication, many affected regions should prioritize reduction of mortality and morbidity before aspiring for elimination

Non-hexagonal neural dynamics in vowel space

Are the grid cells discovered in rodents relevant to human cognition? Following up on two seminal studies by others, we aimed to check whether an approximate 6-fold, grid-like symmetry shows up in the cortical activity of humans who "navigate" between vowels, given that vowel space can be approximated with a continuous trapezoidal 2D manifold, spanned by the first and second formant frequencies. We created 30 vowel trajectories in the assumedly flat central portion of the trapezoid. Each of these trajectories had a duration of 240 milliseconds, with a steady start and end point on the perimeter of a "wheel". We hypothesized that if the neural representation of this "box" is similar to that of rodent grid units, there should be an at least partial hexagonal (6-fold) symmetry in the EEG response of participants who navigate it. We have not found any dominant n-fold symmetry, however, but instead, using PCAs, we find indications that the vowel representation may reflect phonetic features, as positioned on the vowel manifold. The suggestion, therefore, is that vowels are encoded in relation to their salient sensory-perceptual variables, and are not assigned to arbitrary gridlike abstract maps. Finally, we explored the relationship between the first PCA eigenvector and putative vowel attractors for native Italian speakers, who served as the subjects in our study